T03 ma proteinfolding

notebooks/T03_proteinfolding/README.md

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+# T03 · Protein Folding
+
+Authors:
+- Mhd Jawad Al Rahwanji, CADD seminar 2023, Volkamer lab, Saarland University
+- Paula Linh Kramer, 2023, Volkamer lab, Saarland University
+- Andrea Volkamer, 2023, Volkamer lab, Saarland University
+
+
+## Aim of this talktorial
+
+In this notebook, we will learn about protein folding and how to predict protein structures using machine learning. This task is crucial for understanding diseases and accelerating drug development.
+
+
+### Contents in *Theory*
+
+* Protein Folding
+    * Proteins
+    * The Folding Problem
+* History
+    * CASP
+    * Breakthroughs
+* OmegaFold
+    * Inner Workings and Training
+    * Performance Evaluation
+    * More on Orphan Proteins and Antibodies
+    * Investigating the Geoformer
+    * Computational Performance
+* Alternative Methods
+    * Quantum Approach
+    * Diffusion-based Models
+
+
+### Contents in *Practical*
+
+**Goal: Predict the 3D structure of a protein from a given sequence of amino acids and assess the results**
+
+* Overview
+* Setup
+* Processing the Sequences
+* Analyzing the Predictions
+  * 6YJ1
+  * 7FVU
+* Analyzing the Secondary Structures
+  * RMSD
+  * Prediction Confidences
+  * Ramachandran Plots
+* Summary
+
+
+### References
+
+* [CASP](https://predictioncenter.org/)
+* AlphaFold2: [Jumper *et al.*, <i>Nature</i> (2021), <b>596</b>, 583–589](https://doi.org/10.1038/s41586-021-03819-2)
+* RoseTTAFold: [Baek *et al.*, <i>Science</i> (2021), <b>373</b>, 871-876](https://doi.org/10.1126/science.abj8754)
+* OmegaFold: [Wu *et al.*, <i>bioRxiv</i> (2022)](https://doi.org/10.1101/2022.07.21.500999)
+* [Baker lab](https://www.bakerlab.org/)
+* Quantum folding: [Robert *et al.*, <i>npj Quantum Inf.</i> (2021), <b>7</b>, 38](https://doi.org/10.1038/s41534-021-00368-4)
+* Protein generation: [Watson *et al.*, <i>bioRxiv</i> (2022)](https://doi.org/10.1101/2022.12.09.519842)
+* [OmegaFold on Github](https://github.com/HeliXonProtein/OmegaFold)
+* [PDB](https://www.rcsb.org/)
+* [NGLView documentation](http://nglviewer.org/nglview/release/v0.5.1/)
+* [Biopython documentations](https://biopython.org/wiki/Documentation)
+* [Biotite documentation](https://www.biotite-python.org/)

notebooks/T03_proteinfolding/data/README.md

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+# Information about the input files
+
+For each of the following proteins we have a `PDB` and a `FASTA` file stored in the `data` folder. 
+Both of which have been downloaded from the respective source page linked below each of the proteins.
+The `FASTA` file is needed as input to the algorithm we will be using.
+The `PDB` file resembles the ground truth crystalline structure for the protein. 
+It is used to assess the quality of the predicted conformation.
+
+## 6YJ1
+
+### The M23 peptidase domain of the Staphylococcal phage 2638A endolysin
+
+- PDB DOI: https://doi.org/10.2210/pdb6YJ1/pdb
+
+- Classification: VIRAL PROTEIN
+- Organism(s): Staphylococcus phage 2638A
+- Expression System: Escherichia coli
+- Mutation(s): No
+
+- Deposited: 2020-04-02
+- Released: 2020-09-09 
+- Deposition Author(s): Dunne, M., Ernst, P., Sobieraj, A., Pluckthun, A., Loessner, M.J.
+
+#### Experimental Data Snapshot
+
+- Method: X-RAY DIFFRACTION
+- Resolution: 2.30 Å
+- R-Value Free: 0.310 
+- R-Value Work: 0.251 
+- R-Value Observed: 0.254
+
+[Source](https://www.rcsb.org/structure/6yj1)
+
+## 7FVU
+### Crystal Structure of human FABP4 in complex with 2-\[2-(benzothiophen-3-yl)-2,3-dihydrobenzothiophene-3-carbonyl]benzoic acid
+
+- PDB DOI: https://doi.org/10.2210/pdb7FVU/pdb
+
+- Classification: LIPID BINDING PROTEIN
+- Deposition Group: G_1002264
+- Organism(s): Homo sapiens
+- Expression System: Escherichia coli BL21(DE3)
+- Mutation(s): No
+
+- Deposited: 2023-04-27
+- Released: 2023-06-14
+- Deposition Author(s): Ehler, A., Benz, J., Obst, U., Rudolph, M.G.
+- Funding Organization(s): F. Hoffmann-La Roche LTD
+
+#### Experimental Data Snapshot
+
+- Method: X-RAY DIFFRACTION
+- Resolution: 1.24 Å
+- R-Value Free: 0.159
+- R-Value Work: 0.135
+- R-Value Observed: 0.137
+
+[Source](https://www.rcsb.org/structure/7FVU)

notebooks/T03_proteinfolding/data/rcsb_pdb_6YJ1.fasta

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+>6YJ1_1|Chains A, B|ORF007|Staphylococcus phage 2638A (320836)
+MHHHHHHVNSLEMLTAIDYLTKKGWKISSDPRTYDGYPKNYGYRNYHENGINYDEFCGGYHRAFDVYSNETNDVPAVTSGTVIEANDYGNFGGTFVIRDANDNDWIYGHLQRGSMRFVVGDKVNQGDIIGLQGNSNYYDNPMSVHLHLQLRPKDAKKDEKSQVCSGLAMEKYDITNLNAKQDKSKN

notebooks/T03_proteinfolding/data/rcsb_pdb_7FVU.fasta

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+>7FVU_1|Chain A|Fatty acid-binding protein, adipocyte|Homo sapiens (9606)
+GSHMDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKNTEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVMKGVTSTRVYERA